Details of Microbe Species (MIC)

General Information of MIC (ID: MIC01037)
MIC Name Proteobacteria (proteobacteria)
MIC Synonyms Alphaproteobacteraeota; Alphaproteobacteriota
Body Site Nose
Lineage Kingdom: Bacteria
Phylum: Proteobacteria
Oxygen Sensitivity Anaerobe
Microbial Metabolism Fermentative
Gram Negative
Host Relationship Pathogen
Description Proteobacteria is a major phylum of Gram-negative bacteria. It includes a wide variety of pathogenic genera, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia, Legionellales, and many others.
External Links Taxonomy ID
1224
Disease Relevance
          Autism spectrum disorder  [ICD-11: 6A02]
             Description Proteobacteria is upregulated in disease expression of austim. [1]
          Chronic kidney disease  [ICD-11: GB61]
             Description Proteobacterias was the most predominant taxa at the phylum level among different stages of CKD(Chronic kidney disease) patients. [2]
          Crohn disease  [ICD-11: DD70]
             Description Crohns disease-associated microbiota are characterized by the omnipresence of certain Proteobacteria. [3]
          Inflammatory bowel disease  [ICD-11: DD72]
             Description Proteobacteriace is upregulated in disease expression of inflammatory bowel disease. [4]
          Sepsis  [ICD-11: 1G41]
             Description Sepsis was associated with Proteobacteria infection. [5]
          Type 2 diabetes mellitus  [ICD-11: 5A11]
             Description The intestinal microbiota across the subjects with type 2 diabetes was relatively enriched with Proteobacteria. [6]
          Ulcerative colitis  [ICD-11: DD71]
             Description The differences at the phylum level between the Ulcerative colitis and Familial adenomatous polyposis cohorts corresponded to significant increases in the levels of the proteobacterial families Comamonadaceae, Moraxellaceae and Alcaligenaceae in tandem with a significant reduction in the Bacteroidetes families Bacteroidaceae and Prevotellaceae and the Firmicutes family Ruminococcaceae in Ulcerative colitis. [7]
Host Genetic Factors (HGFs)
          TLR4
             HGF ID HGF2320 HGF Info       Class Copy Number Variation: Gene Duplication (CNV-GDu)
             Description The overexpression of TLR4 increased the abundance of Proteobacteria. [8]
          TLR2
             HGF ID HGF2319 HGF Info       Class Copy Number Variation: Gene Deletion (CNV-GDe)
             Description The deletion of TLR2 was significantly associated with a decrease in the Bacteroidetes phyla (p-value<0.05). [9]
          SHANK3
             HGF ID HGF2351 HGF Info       Class Copy Number Variation: Gene Deletion (CNV-GDe)
             Description The deletion of SHANK3 has been significantly associated with the decreased amount of Proteobacteria (p-value<0.05). [10]
          hsa-miR-181a-5p
             HGF ID HGF0237 HGF Info       Class Non-coding RNA: Micro (ncRNA-miRNA)
             Description The hsa-miR-181a-5p was significantly associated with the abundance of Proteobacteria (p-value<0.05). [11]
          hsa-miR-21-5p
             HGF ID HGF0204 HGF Info       Class Non-coding RNA: Micro (ncRNA-miRNA)
             Description The miR-21 was significantly associated with the abundance of Proteobacteria (p-value<0.05). [11]
          mmu-miR-666-5p
             HGF ID HGF0018 HGF Info       Class Non-coding RNA: Micro (ncRNA-miRNA)
             Description The mmu-miR-666-5p was significantly associated with the abundance of Proteobacteria (p-value<0.05). [11]
          hsa-miR-200a-3p
             HGF ID HGF0213 HGF Info       Class Non-coding RNA: Micro (ncRNA-miRNA)
             Description The level of miR-200a-3p was substantially correlated with the relative abundance of Proteobacteria. [12]
          rs9323326
             HGF ID HGF1918 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs9323326 SNP was significantly associated with the abundance of Proteobacteria (p-value=8.76E-10). [13]
          rs927984
             HGF ID HGF1884 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs927984 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=2.78E-07). [14]
          rs7749517
             HGF ID HGF2020 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs7749517 SNP was significantly associated with the abundance of Proteobacteria (p-value=8.01E-08). [15]
          rs7702475
             HGF ID HGF1391 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs7702475 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=2.46E-07). [14]
          rs7134375
             HGF ID HGF1645 HGF Info       Class Single Nucleotide Polymorphism: Non coding transcript variant (SNP-NCTV)
             Description The rs7134375 SNP was significantly associated with the abundance of Proteobacteria (p-value=6.70E-05 ). [16]
          rs6581319
             HGF ID HGF2227 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs6581319 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=2.83E-04). [14]
          rs61746477
             HGF ID HGF1825 HGF Info       Class Single Nucleotide Polymorphism: Synonymous variant (SNP-SV)
             Description The rs61746477 SNP was significantly associated with the abundance of Proteobacteria (p-value=3.56E-07). [17]
          rs6021
             HGF ID HGF1786 HGF Info       Class Single Nucleotide Polymorphism: Synonymous variant (SNP-SV)
             Description The rs6021 SNP was significantly associated with the abundance of Proteobacteria (p-value=1.51E-06). [17]
          rs516246
             HGF ID HGF1582 HGF Info       Class Single Nucleotide Polymorphism: Non coding transcript variant (SNP-NCTV)
             Description The rs516246 SNP was significantly associated with the abundance of Proteobacteria (p-value=0.02994). [18]
          rs4598262
             HGF ID HGF1987 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs4598262 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=4.83E-07). [14]
          rs358580
             HGF ID HGF1699 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs358580 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=3.05E-03). [14]
          rs35205675
             HGF ID HGF2169 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs35205675 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=5.16E-07). [14]
          rs3219487
             HGF ID HGF1496 HGF Info       Class Single Nucleotide Polymorphism: Non coding transcript variant (SNP-NCTV)
             Description The rs3219487 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=3.05E-06). [14]
          rs2925216
             HGF ID HGF2135 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs2925216 SNP was significantly associated with the relative abundance of Proteobacteria (p-value=3.65E-09). [19]
          rs2290717
             HGF ID HGF1306 HGF Info       Class Single Nucleotide Polymorphism: Missense variant (SNP-MV)
             Description The rs2290717 SNP was significantly associated with the abundance of Proteobacteria (p-value=6.79E-06). [17]
          rs2166343
             HGF ID HGF2041 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs2166343 SNP is significantly associated with the abundance of gut microbiota Proteobacteria (p-value<5.00E-05). [20]
          rs17783344
             HGF ID HGF1759 HGF Info       Class Single Nucleotide Polymorphism: Missense variant (SNP-MV)
             Description The rs17783344 SNP was significantly associated with the abundance of Proteobacteria (p-value=3.67E-06). [17]
          rs1653301
             HGF ID HGF2132 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs1653301 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=4.93E-03). [14]
          rs1543603
             HGF ID HGF1883 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs1543603 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=3.31E-07). [14]
          rs13214269
             HGF ID HGF2021 HGF Info       Class Single Nucleotide Polymorphism (SNP)
             Description The rs13214269 SNP was significantly associated with the abundance of Proteobacteria (p-value=3.01E-07). [15]
          rs12313
             HGF ID HGF1816 HGF Info       Class Single Nucleotide Polymorphism: Synonymous variant (SNP-SV)
             Description The rs12313 SNP was significantly associated with the abundance of Proteobacteria (p-value=2.54E-06). [17]
          rs12137699
             HGF ID HGF1242 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs12137699 SNP was significantly associated with the abundance of Proteobacterial (p-value=4.58959E-05). [21]
          rs1208083
             HGF ID HGF1506 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs1208083 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=1.09E-06). [14]
          rs11651784
             HGF ID HGF1337 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs11651784 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=1.08E-05). [14]
          rs111278434
             HGF ID HGF1771 HGF Info       Class Single Nucleotide Polymorphism: Intron variant (SNP-IV)
             Description The rs111278434 SNP in mucosal immunity pathways influences the abundance of Proteobacteria in the upper airway (p-value=4.66E-07). [14]
          rs1053985
             HGF ID HGF1366 HGF Info       Class Single Nucleotide Polymorphism: Synonymous variant (SNP-SV)
             Description The rs1053985 SNP was significantly associated with the abundance of Proteobacteria (p-value=3.51E-06). [17]
Host Immune Factors (HIFs)
          C-C motif chemokine 13
             HIF ID HIFM0018 HIF Info       Class Antimicrobial peptide (AMP)
             Description The phylum Proteobacteria was correlated with the expression of CCL13. [22]
          Interferon-6
             HIF ID HIFM0151 HIF Info       Class Cytokine (Cyt)
             Description Increased abundance of the phyla Proteobacteria is associated with the enriched concentrations of IL-6 in serum. [23]
          Immunoglobulin A
             HIF ID HIFM0272 HIF Info       Class Immunoglobulin (Ig)
             Description Serum IgAs has regulatory affinity which could bind prominently to Proteobacterial taxa. [24]
          Immunoglobulin A1
             HIF ID HIFM0275 HIF Info       Class Immunoglobulin (Ig)
             Description IgA1 has regulatory affinity which could bind prominently to Proteobacterial taxa. [24]
          Nuclear receptor ROR-beta
             HIF ID HIFM0204 HIF Info       Class Retinoic acid receptor (RAR)
             Description Alteration of the gut Proteobacteria resulted in increased expression of the effector gene Ror-beta. [25]
Environmental Factor(s)
             Disbiome ID
      221
             gutMDisorder ID
      gm0545
References
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2 Gut Microbiota as Diagnostic Tools for Mirroring Disease Progression and Circulating Nephrotoxin Levels in Chronic Kidney Disease: Discovery and Validation Study. Int J Biol Sci. 2020 Jan 1;16(3):420-434. doi: 10.7150/ijbs.37421. eCollection 2020.
3 Debugging the intestinal microbiota in IBD. Gastroenterol Clin Biol. 2009 Jun;33 Suppl 3:S131-6. doi: 10.1016/S0399-8320(09)73148-3.
4 Dysbiosis in the pathogenesis of pediatric inflammatory bowel diseases. Int J Inflam. 2012;2012:687143. doi: 10.1155/2012/687143. Epub 2012 May 20.
5 Gut microbial colonisation in premature neonates predicts neonatal sepsis. Arch Dis Child Fetal Neonatal Ed. 2012 Nov;97(6):F456-62. doi: 10.1136/fetalneonatal-2011-301373. Epub 2012 May 6.
6 Gut microbiota in human adults with type 2 diabetes differs from non-diabetic adults. PLoS One. 2010 Feb 5;5(2):e9085. doi: 10.1371/journal.pone.0009085.
7 The bacteriology of pouchitis: a molecular phylogenetic analysis using 16S rRNA gene cloning and sequencing. Ann Surg. 2010 Jul;252(1):90-8. doi: 10.1097/SLA.0b013e3181e3dc8b.
8 Current understanding of the gut microbiota shaping mechanisms.J Biomed Sci. 2019 Aug 21;26(1):59. doi: 10.1186/s12929-019-0554-5.
9 Microbiota determines insulin sensitivity in TLR2-KO mice.Life Sci. 2019 Oct 1;234:116793. doi: 10.1016/j.lfs.2019.116793. Epub 2019 Aug 26.
10 Altered Intestinal Morphology and Microbiota Composition in the Autism Spectrum Disorders Associated SHANK3 Mouse Model.Int J Mol Sci. 2019 Apr 30;20(9):2134. doi: 10.3390/ijms20092134.
11 Associations between hepatic miRNA expression, liver triacylglycerols and gut microbiota during metabolic adaptation to high-fat diet in mice. Diabetologia. 2017 Apr;60(4):690-700. doi: 10.1007/s00125-017-4209-3. Epub 2017 Jan 19.
12 Vascular microRNA-204 is remotely governed by the microbiome and impairs endothelium-dependent vasorelaxation by downregulating Sirtuin1. Vikram A, Kim YR, Kumar S, Li Q, Kassan M, Jacobs JS, Irani K.. Nat Commun. 2016 Sep 2;7:12565. doi: 10.1038/ncomms12565.
13 Genome-wide association analysis identifies variation in vitamin D receptor and other host factors influencing the gut microbiota.Nat Genet. 2016 Nov;48(11):1396-1406. doi: 10.1038/ng.3695. Epub 2016 Oct 10.
14 Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.Microbiome. 2017 Feb 1;5(1):16. doi: 10.1186/s40168-016-0227-5.
15 Genetic Determinants of the Gut Microbiome in UK Twins.Cell Host Microbe. 2016 May 11;19(5):731-43. doi: 10.1016/j.chom.2016.04.017.
16 The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.Circ Res. 2015 Oct 9;117(9):817-24. doi: 10.1161/CIRCRESAHA.115.306807. Epub 2015 Sep 10.
17 Host genetic variation impacts microbiome composition across human body sites.Genome Biol. 2015 Sep 15;16(1):191. doi: 10.1186/s13059-015-0759-1.
18 FUT2 genotype and secretory status are not associated with fecal microbial composition and inferred function in healthy subjects.Gut Microbes. 2018 Jul 4;9(4):357-368. doi: 10.1080/19490976.2018.1445956. Epub 2018 Apr 27.
19 Association of host genome with intestinal microbial composition in a large healthy cohort.Nat Genet. 2016 Nov;48(11):1413-1417. doi: 10.1038/ng.3693. Epub 2016 Oct 3.
20 Assessing the Relationship Between Gut Microbiota and Bone Mineral Density.Front Genet. 2020 Jan 31;11:6. doi: 10.3389/fgene.2020.00006. eCollection 2020.
21 The effect of host genetics on the gut microbiome.Nat Genet. 2016 Nov;48(11):1407-1412. doi: 10.1038/ng.3663. Epub 2016 Oct 3.
22 Duodenal Mucosa of Patients With Type 1 Diabetes Shows Distinctive Inflammatory Profile and Microbiota.J Clin Endocrinol Metab. 2017 May 1;102(5):1468-1477. doi: 10.1210/jc.2016-3222.
23 Prebiotic, immuno-stimulating and gut microbiota-modulating effects of Lycium barbarum polysaccharide. Biomed Pharmacother. 2020 Jan;121:109591. doi: 10.1016/j.biopha.2019.109591. Epub 2019 Nov 13.
24 IgA Responses to Microbiota.Immunity. 2018 Aug 21;49(2):211-224. doi: 10.1016/j.immuni.2018.08.011.
25 Metronidazole Causes Skeletal Muscle Atrophy and Modulates Muscle Chronometabolism. Int J Mol Sci. 2018 Aug 16;19(8):2418. doi: 10.3390/ijms19082418.

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